The plots for this series were, at the time of its initial airing, arguably the best effort to portray comic book heroes in animated television shorts. As originally aired, this season consisted of two half-hour segments. The first of these featured the Legion of Doom, a team of thirteen recurring foes, the Super Friends' worst enemies. Every episode would feature battles between the thirteen supervillains of the Legion of Doom and the eleven superheroes of the Justice League of America. The Legion of Doom dwelled in a murky swamp and launched their attacks for global conquest from a sinister looking, swamp-based, mechanical flying headquarters called the Hall of Doom (which also resembled Darth Vader's helmet) as a suitable contrast with the Super Friends' gleaming Hall of Justice.

The second segment of this season was an adventure with Superman, Batman and Robin, Wonder Woman, Aquaman, and the Wonder Twins, similar to those that had aired the previous season in The All-New Super Friends Hour.[1] Thanks to these episodes being shown using the opening credits of the All-New Super Friends Hour in syndication,[2] the second segment along being used with the Challenge of Super Friends opening, and confused references to the show[3] it is often mistakenly believed that the first and second segments were two separate shows.

Bill Woodson provides the uncredited voice of the narrator in Challenge of the Super Friends. The show's main theme and original music was composed and arranged by musical director Hoyt Curtin. The music supervisor was Paul DeKorte. Character designs for this particular Super Friends series were done by Andre LeBlanc.

Despite the claim in the program's title sequence that the Legion's members hail from "remote galaxies", only Brainiac and Sinestro are extraterrestrials; the remaining members are all natives of Earth (Even though Bizarro called Bizarro World home he was created by Lex Luthor via duplicator ray on Earth technically making him a 'native' of Earth)

Warner Home Video originally released this season of Super Friends on two separate DVDs on June 1, 2004. The first one being "Challenge of the Super Friends: Attack of the Legion of Doom", which featured the "Challenge" segments, and the second being Challenge of the Super Friends: United They Stand", which featured the Super Friends segments. Both DVDs only featured four episodes. The first season was re-released as "Challenge of the Super Friends: The First Season" on July 6, 2004. The second season was re-released as "Super Friends: Volume Two" on May 24, 2005. Both of these DVDs were a box set with all sixteen episodes.

Cartoon Network produced a couple of commercials spoofing Challenge of the Super Friends.

One dealt with the idiosyncratic nature of the Legion of Doom and Brainiac’s odd manner of dress (Brainiac: “Look, I just want some pants...a decent pair of pants!” Solomon Grundy: “Solomon Grundy want pants, too!”).

The second, co-starring The Powerpuff Girls, dealt with Aquaman’s powers (Aquaman: “My ability to talk to fish is of no use to us, Wonder Woman!”) as well as the level of violence compared to today’s cartoons, as Wonder Woman and Aquaman look away while the Powerpuff Girls beat up the Legion of Doom, going so far as to set the Scarecrow on fire. Most notably was Bubbles' double-entendre reply to Wonder Woman's compliment on how they were developing as superheroes. "Someday we'll be as developed as you." Lex Luthor, as a villain with a dirty mind, began laughing. His underlings understood the joke and laughed as well. When a piece of the Hall of Doom's ceiling fell on Luthor's head, everyone laughed.

The opening sequence of the Robot ChickenDC Comics Special parodies the opening of Challenge of the Super Friends with the Legion of Doom substituted for Robot Chicken original characters Chicken, Mad Scientist, Nerd, Humping Robot, Composite Santa, Gummy Bear, the Unicorn, and Bitch Puddin'. The Legion of Doom, Hall of Doom, and Hall of Justice also feature prominently in the episode.